ParsEval Code
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danielstandage
File | Date | Author | Commit |
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data | 2012-08-03 |
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[3b899e] Merge branch 'master' of ssh://parseval.git.sou... |
docs | 2012-05-16 |
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[da44b0] Updated docs |
inc | 2012-08-02 |
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[953c37] Substantial refactoring |
src | 2013-07-24 |
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[5cf772] Fix for GT 1.5.1 compatibility |
CONTRIBUTORS | 2012-08-03 |
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[aa5ba7] Corrected license and attributions |
LICENSE | 2012-08-03 |
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[aa5ba7] Corrected license and attributions |
README | 2012-08-03 |
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[aa5ba7] Corrected license and attributions |
makefile | 2012-08-02 |
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[953c37] Substantial refactoring |
This directory contains the source code for ParsEval version 0.9.1. Copyright (c) 2010-2012, Daniel S. Standage and CONTRIBUTORS See CONTRIBUTORS and LICENSE or http://parseval.sourceforge.net/license.txt for details. ParsEval is a program for comparing distinct sets of gene structure annotations for the same sequence(s). This program calculates and reports a rich set of comparison statistics, both at the level of individual gene loci as well as at the level of entire sequences. Please cite ParsEval as follows. Standage, Daniel S. and Volker P. Brendel (2012) ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics, 13:187. -------------------------------------------------------------------------------- Installation instructions for the impatient -------------------------------------------------------------------------------- If you have root access to a Linux system, chances are you can simply run the commands below to install ParsEval. I provide commands as would be run in the Ubuntu distribution. Similar commands should be available for any other Linux distribution. If you're not running Linux, or if you run into any problems following these commands, you should probably take some time to read through the rest of the installation instructions before proceeding. # Run as root sudo bash # System environment configuration (platform-dependent) # See `docs' directory for platform-specific configuration instructions echo $PATH | grep /usr/local/bin || (export PATH=/usr/local/bin:$PATH && / echo 'export PATH=/usr/local/bin:$PATH' >> /etc/bash.bashrc) test -d /usr/local/src || mkdir -p /usr/local/src grep '/usr/local/lib' /etc/ld.so.conf || / (echo '/usr/local/lib' >> /etc/ld.so.conf && ldconfig) apt-get install -y build-essential git libcairo2-dev libncurses5-dev # Install GenomeTools and ParsEval (platform-independent) cd /usr/local/src git clone git://genometools.org/genometools.git cd genometools make 64bit=yes make install cd /usr/local/src git clone git://parseval.git.sourceforge.net/gitroot/parseval/parseval cd parseval make 64bit=yes make install # Test ParsEval: print usage statement parseval -h -------------------------------------------------------------------------------- Prerequisites -------------------------------------------------------------------------------- In principle, ParsEval should compile and run on any POSIX-compliant UNIX system (Linux, Mac OS X, Cygwin), although in practice, it has only been tested on Linux and Mac systems. Native Windows support is not anticipated any time soon. The ParsEval developers have made an effort to minimize dependency on external software, but compiling and installing does require a few prerequisites. First, the system must include common Unix tools for building software: specifically, GNU make (version 3.80 or later) and a C compiler with OpenMP support (e.g. GCC 4.2 or higher). Additionally, the system must have the GenomeTools library installed (see http://genometools.org/ for download and installation instructions). To fully take advantage of the graphics capabilities provided by GenomeTools, the system must also have an installation of the Cairo graphics library (see the GenomeTools documentation). -------------------------------------------------------------------------------- Compiling and installing -------------------------------------------------------------------------------- It is generally assumed that the user will follow standard Linux/Unix procedures when downloading, compiling, and installing the GenomeTools prerequisite. The default install directory is `/usr/local', which means that we assume the GenomeTools source code has been placed in `/usr/local/src/', the binaries have been installed in `/usr/local/bin', the shared libraries have been installed in `/usr/local/lib', and so forth. If this is the case, then the installation procedure described above should work just fine. From the directory containing the ParsEval source code distribution, enter the following commands. make make install # requires root access If you have some reason to install GenomeTools in some other directory (e.g. if you don't have permissions to modify `/usr/local'), this should not be a problem for ParsEval. You must simply tell ParsEval where to find GenomeTools. For example, if you installed GenomeTools in `/home/alice/local', then you must indicate this fact when compiling ParsEval. The following `make' options are available if you encounter any problems during installation or if you want to customize your installation. - 64bit=yes if you want compile for a 64-bit architecture - cairo=no if your system does not have Cairo graphics libraries installed (you will not be able to generate graphics) - GT_INSTALL_DIR=? if you did not install GenomeTools in `/usr/local' - GT_COMPILE_DIR=? if you did not download and compile GenomeTools in `/usr/local/src/genometools' - prefix=? to install ParsEval in a directory other than `/usr/local' (e.g. if you do not have admin privileges) For example, if I need to install GenomeTools and ParsEval in my home directory (`/home/alice'), then I could do something like this. test -d /home/alice/local/src || mkdir -p /home/alice/local/src cd /home/alice/local/src git clone git://genometools.org/genometools.git cd genometools make prefix=/home/alice/local 64bit=yes make prefix=/home/alice/local 64bit=yes install cd /home/alice/local/src git clone git://parseval.git.sourceforge.net/gitroot/parseval/parseval cd parseval make prefix=/home/alice/local GT_INSTALL_DIR=/home/alice/local / GT_COMPILE_DIR=/home/alice/local/src/genometools 64bit=yes make prefix=/home/alice/local GT_INSTALL_DIR=/home/alice/local / GT_COMPILE_DIR=/home/alice/local/src/genometools 64bit=yes install Remember that if you install the GenomeTools library in a non-standard location, you will need to make sure that the ParsEval program can find that library at runtime. This can be done on a temporary basis using the `LD_LIBRARY_PATH' environmental variable or on a permanent system-wide basis using the `ldconfig' command. Although the `/usr/local' directory is the standard install location for 3rd party libraries, on some distributions this directory is not pre-configured. If you use the default install locations and still run into problems, make sure that `/usr/local/bin' is in your path (using the `export' or `setenv' commands) and that `/usr/local/lib' is in the LD path (using the `ldconfig' command). -------------------------------------------------------------------------------- Running ParsEval -------------------------------------------------------------------------------- Invoking `parseval -h' will print a helpful usage statement to the terminal. Also, see data/benchmarks/README for several examples demonstrating ParsEval's features. -------------------------------------------------------------------------------- Contact -------------------------------------------------------------------------------- If you have any questions regarding ParsEval, feel free to contact the authors using the ParsEval mailing list (parseval-users@lists.sourceforge.net) or by direct email (daniel.standage@gmail.com).